2009
The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules
Sproviero EM, Newcomer MB, Gascón JA, Batista ER, Brudvig GW, Batista VS. The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules. Photosynthesis Research 2009, 102: 455-470. PMID: 19633920, PMCID: PMC2954272, DOI: 10.1007/s11120-009-9467-6.Peer-Reviewed Original ResearchConceptsElectrostatic interactionsMM methodQuantum mechanics/molecular mechanics (QM/MM) hybrid methodsForce fieldQM/MM hybrid methodsQM/MM methodologyQM/MM methodsMolecular mechanics force fieldQuantum chemistry techniquesMM force fieldsStructural refinementPhotosystem IIChemistry techniquesStructure/function relationsCharge transferQM layerMolecular fragmentsChemical modificationBiological macromoleculesSteric hindranceComputational protocolSpectroscopic dataMolecular domainsStructural propertiesHigh-resolution spectroscopic data
2005
A Self-Consistent Space-Domain Decomposition Method for QM/MM Computations of Protein Electrostatic Potentials
Gascon J, Leung S, Batista E, Batista V. A Self-Consistent Space-Domain Decomposition Method for QM/MM Computations of Protein Electrostatic Potentials. Journal Of Chemical Theory And Computation 2005, 2: 175-186. PMID: 26626392, DOI: 10.1021/ct050218h.Peer-Reviewed Original ResearchProtein electrostatic potentialElectrostatic potentialElectrostatic potential atomic chargesPolarization effectsCorresponding electrostatic potentialFull QM calculationsMutual polarization effectsMM force fieldsPoint charge modelQM calculationsQuantitative agreementAtomic chargesForce fieldMolecular domainsProtein environmentProtein-protein electrostatic interactions